schrodinger.protein.alignment module

Classes for working with sequences containing alignment information (gaps) and collections thereof.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.protein.alignment.ResidueSelection(residues, indices)

Bases: tuple

indices

Alias for field number 1

residues

Alias for field number 0

exception schrodinger.protein.alignment.AnchoredResidueError

Bases: RuntimeError

exception schrodinger.protein.alignment.StructuredResidueError

Bases: RuntimeError

class schrodinger.protein.alignment.AlignmentSignals

Bases: PyQt5.QtCore.QObject

A collection of signals that can be emitted by an alignment

Variables:
  • sequencesAboutToBeInserted (QtCore.pyqtSignal) – A signal emitted before sequences are inserted into the alignment. Emitted with: (The index of the first sequence to be inserted, The index of the last sequence to be inserted)
  • sequencesInserted (QtCore.pyqtSignal) – A signal emitted after sequences are inserted into the alignment. Emitted with: (The index of the first sequence inserted, The index of the last sequence inserted)
  • sequencesAboutToBeRemoved (QtCore.pyqtSignal) – A signal emitted before sequences are removed from the alignment. Emitted with: (The index of the first sequence to be removed, The index of the last sequence to be removed)
  • sequencesRemoved (QtCore.pyqtSignal) – A signal emitted after sequences are removed from the alignment. Emitted with: (The index of the first sequence removed, The index of the last sequence removed)
  • sequenceResiduesChanged (QtCore.pyqtSignal) – A signal emitted after the contents of a sequence have changed. Note that this signal may also be emitted in response to a sequence changing length, as positions in the alignment may switch from blank to occupied or vice versa. Emitted with: (The modified sequence, The position of the first modified residue, The position of the last modified residue)
  • sequencesAboutToBeReordered – Signal emitted before reordering sequences
  • sequencesReordered – Signal emitted after sequences have been reordered
  • sequenceNameChanged (QtCore.pyqtSignal) – A signal emitted after a sequence has changed names. Emitted with: (The modified sequence)
  • annotationTitleChanged (QtCore.pyqtSignal) – A signal emitted after a sequence’s annotation has changed titles. Emitted with: (The sequence whose annotation title has been modified)
  • alignmentNumColumnsAboutToChange (QtCore.pyqtSignal) – A signal emitted before the alignment changes length. Emitted with: (The current length of the alignment, The new length of the alignment)
  • alignmentNumColumnsChanged (QtCore.pyqtSignal) – A signal emitted after the alignment changes length. Emitted with: (The old length of the alignment, The current length of the alignment)
  • residuesAboutToBeRemoved (QtCore.pyqtSignal) – A signal emitted before residues are to be removed. Emitted with a list of the residues to be removed.
  • residuesRemoved (QtCore.pyqtSignal) – A signal emitted after residues are removed. This signal is not emitted with any parameters, but the residues that were removed were listed with the corresponding residuesAboutToBeRemoved signal.
  • residuesAdded (QtCore.pyqtSignal) – A signal emitted with added residues. Note that this signal will be only be emitted once even if residues are added to multiple sequences. In addition, each individual sequence will emit a lengthChanged signal.
  • sequenceVisibilityChanged (QtCore.pyqtSignal) – A signal emitted when visibility of a sequence changes. Emitted with: (the sequence whose visibility is changing, the index of the sequence)
  • sequenceStructureChanged (QtCore.pyqtSignal) – A signal emitted when structure of a sequence changes. Emitted with: (the sequence whose visibility is changing, the index of the sequence)
  • alignmentAboutToBeCleared (QtCore.pyqtSignal) – A signal emitted just before all sequences are removed from the alignment.
  • alignmentCleared (QtCore.pyqtSignal) – A signal emitted just after all sequences have been removed from the alignment.
  • anchoredResiduesChanged – A signal emitted when one or more residues are anchored or unanchored.
Type:

sequencesAboutToBeReordered: QtCore.pyqtSignals
Type:

sequencesReordered: QtCore.pyqtSignals
sequencesAboutToBeInserted
sequencesInserted
sequencesAboutToBeRemoved
sequencesRemoved
sequenceResiduesChanged
sequencesAboutToBeReordered
sequencesReordered
sequenceNameChanged
annotationTitleChanged
alignmentNumColumnsAboutToChange
alignmentNumColumnsChanged
residuesAboutToBeRemoved
residuesRemoved
residuesAdded
sequenceVisibilityChanged
sequenceStructureChanged
alignmentAboutToBeCleared
alignmentCleared
anchoredResiduesChanged
emitSeqResChanged(first_res, last_res)
emitSeqNameChanged()
emitAnnTitleChanged()
class schrodinger.protein.alignment.BaseAlignment(sequences=None)

Bases: PyQt5.QtCore.QObject

Abstract base class for classes which handle alignment of various sequences and corresponding annotations.

This is a pure domain object intended to make it easy to work with aligned collections of sequences.

Some methods are decorated with @msv_utils.const in order to make it easy to write a wrapper for this class that supports undo/redo operations.

global_annotations

Returns the alignment-level annotations available for the alignment

seq_annotations

Returns the sequence-level annotations available for sequences held in the alignment

all_annotations

Return a list of all annotations types in this alignment

iterResidues()

Yields a sequence of schrodinger.protein.residue.Residue objects in the alignment, omitting gaps.

getGlobalAnnotationData(index, annotation)

Returns column-level annotation data at an index in the alignment

Parameters:
  • index (int) – The index in the alignment
  • annotation (enum.Enum) – An enum representing the requested annotation, if any
num_columns
getWorkspaceCounts()

Summarize the visibility status of the alignment’s sequences

Returns:Counts of each type of visibility
Return type:collections.Counter
index(seq)

Returns the index of the specified sequence.

Parameters:seq (sequence.Sequence) – The requested sequence
Return type:int
Returns:The index of the requested sequence
reorderSequences(seq_indices)

Reorder the sequences in the alignment using the specified list of indices.

In the undoable version of this class, the private function is needed to perform the operation in an undoable operation.

Parameters:seq_indices – A list with the new indices for sequences
Type:list of int
Raises:ValueError – In the event that the list of indices does not match the length of the alignment
sort(*, key, reverse=False)

Sort the alignment by the specified criteria.

NOTE: Query sequence is not included in the sort.

Parameters:
  • key (function) – A function that takes a sequence and returns a value to sort by for each sequence. (required keyword-only argument)
  • reverse (bool) – Whether to sort in reverse (descending) order.
addSeq(seq, index=None)
Parameters:
  • seq (sequence.Sequence) – The sequence to add
  • start (int) – The index at which to insert; if None, seq is appended
addSeqs(sequences, start=None)

Add multiple sequences to the alignment

Parameters:
  • sequences (list of sequence.Sequence) – Sequences to add
  • start (int) – The index at which to insert; if None, seqs are appended
addSeqsByIndices(seq_index_map)

Insert a sequences at the specified indices in the alignment. The sequences will be added from lowest to highest to allow for specification of indexes that may be out of range of the current alignment until lower-indexed sequences have been added. Note that indexes that remain out of range will result in their corresponding sequence simply being appended to the end of the alignment.

Parameters:seq_index_map – Map of insertion indices to sequences to be added.
removeSeq(seq)

Remove a sequence from the alignment

Parameters:seq (sequence.Sequence) – The sequence to remove
removeSeqs(seqs)

Remove multiple sequences from the alignment

removeSeqByIndex(index)

Remove a Sequence from the alignment

Parameters:index (int) – The index of the sequence to remove
replaceSeq(seq, index)

Replace the sequence at the specified index with the elements in the specified sequence

Note that this leaves the original sequence itself intact so that it continues to be monitored

Parameters:
  • seq (iterable of schrodinger.protein.residue. Residue) – The sequence whose elements we use
  • index (int) – The index of the sequence to replace
addOrReplaceSeqs(seqs, identifier_func)

Given seqs and an identifier_func, replaces seqs in the alignment matching the identifier_func and appends any additional seqs to the alignment

Parameters:
  • seqs (iterable of schrodinger.protein.sequence. Sequence) – The sequences to add to the alignment
  • identifier_func (callable) – A key function to uniquely identify sequences
clear()

Clears the entire alignment of sequences

setReferenceSeq(seq)

Set the specified sequence as the reference sequence.

Parameters:seq (sequence) – Sequence to set as reference sequence
getReferenceSeq()

Returns the sequence that has been set as reference sequence or None if there is no reference sequence.

Returns:The reference sequence or None
Return type:Sequence or None
isReferenceSeq(seq)

Return whether or not a sequence is the reference sequence.

Parameters:seq (Sequence) – Sequence to check
Returns:True if the sequence is the reference sequence, False otherwise.
Return type:bool
getResidueIndices(residues)

Returns the indices (in the alignment) of the specified residues

Parameters:residues (list[residue.AbstractSequenceElement]) – The list of residues and gaps to get indices for.
Return type:A sorted list of (sequence index, residue index) tuples
Returns:list[tuple(int, int)]
makeResidueSelection(residues)

Returns a residue selection object matching the specified residues

Parameters:residues (list) – A list of residues
Return type:ResidueSelection
Returns:An object containing selection information
removeElements(elements)

Removes the specified elements from the alignment.

Parameters:

elements (iterable(residue.AbstractSequenceElement)) – An iterable of elements.
Raises:
mutateResidues(seq_i, start, end, elements)

Mutate a sequence.

Parameters:
  • seq_i (int) – Index of seq to mutate
  • start (int) – Start index of seq region to mutate
  • end (int) – End index of seq region to mutate
  • elements (iterable(str) or iterable(ElementClass)) – Elements to mutate to
Raises:
replaceResiduesWithGaps(residues)

Replaces the specified residues with gaps

Parameters:residues (list) – A list of residues to replace with gaps
addElements(seq, res_i, elements)

Adds the specified elements (residues and/or gaps) to the alignment.

Parameters:
modifyingStructure()
suspendAnchors()

While inside this context, all anchors will be ignored. Upon exit, the anchors will be restored and an exception will be raised if any of the anchors are not aligned to the same reference residues they were aligned to at the start.

anchorResidues(residues)

Anchor the specified residues. If passed reference residues, all residues aligned to the reference residues will be anchored.

Anchored residues are constrained to stay aligned to the reference residue with the same column index at the time of anchoring. If elements are removed from the alignment, gaps are added before anchors to maintain alignment. If any other modifications are made to the alignment that would break an anchor, an exception is raised. However, calling code can temporarily take responsibility for maintaining the anchors within the suspendAnchors context.

Parameters:residues (list(residue.Residue)) – Residues to anchor.
getAnchoredResidues()
Returns:A frozenset of residues that are currently anchored.

:rtype : frozenset(residue.Residue)

getAnchoredResiduesWithRef()
Returns:A frozenset of residues that are currently anchored with the corresponding reference sequence residues

:rtype : frozenset(residue.Residue)

clearAnchors()
removeAnchors(residues)

Unanchor residues. If passed reference residues, all residues anchored to those reference residues will be unanchored.

Parameters:residues (iterable(residue.Residue)) – The residues to unanchor.
Raises:ValueError – When a residue is passed in that isn’t currently anchored.
getSubalignment(start, end)

Return another alignment containing the elements within the specified start and end indices

Parameters:
  • start (int) – The index at which the subalignment should start
  • end (int) – The index at which the subalignment should end (exclusive)
Return type:

BaseAligment
Returns:

An alignment corresponding to the start and end point specified
getDiscontinuousSubalignment(indices)

Given a list of indices, return a new alignment of sequences made up of the residues at those specified indices within this alignment.

Parameters:indices (list of (int, int)) – List of (seq index, residue index) tuples
Returns:A new subalignment
Return type:BaseAlignment
removeSubalignment(start, end)

Remove a block of the subalignment from the start to end points.

Parameters:
  • start (int) – The start index of the columns to remove
  • end (int) – The end index of the columns to remove (exclusive)
is_rectangular
insertSubalignment(aln, start)

Insert an alignment into the current alignment at the specified index

Parameters:
  • aln (BaseAlignment) – The alignment to insert
  • start (int) – The index at which to insert the alignment
Raises:

ValueError – if either alignment is not rectangular
replaceSubalignment(aln, start, end)

Replace a subsection of the alignment indicated by start and end indices with the specified alignment

Parameters:
  • aln (BaseAlignment) – The alignment to insert
  • start (int) – The starting index of the subsection to replace.
  • end (int) – The ending index of the subsection to replace.
Raises:

ValueError – if either alignment is not rectangular
getGaps()

Returns a list of list of gaps.

Returns:list(list(residue.Gap))
Return type:list
getTerminalGaps()

Returns the terminal gaps in all the sequences

Return type:list
Returns:list(list(residue.Gap))
removeAllGaps()

Removes all the gaps of the sequences in the alignment.

removeTerminalGaps()

Removes the gaps from the ends of every sequence in the alignment

addGapsByIndices(gap_indices)

Adds gaps to the alignment

Note:

the length of the gap_indices list must match the number of sequences in the alignment.
Parameters:

gap_indices (list[list[int]]) – A list of lists of gap indices, one for each sequence in the alignment. Note that these indices are based on residue/gap numbering after the insertion. To insert gaps using indices based on numbering before the insertion, see addGapsBeforeIndices.
Raises:
  • ValueError – if gap_indices is the wrong length
  • AnchoredResidueError – if any gap index is before an anchored col
addGapsBeforeIndices(indices)

Add one gap to the alignment before each of the specified residue positions.

Note:the length of the gap_indices list must match the number of sequences in the alignment.
Parameters:indices – A list of lists of indices to insert gaps before, one for each sequence in the alignment. Note that these indices are based on residue/gap numbering before the insertion. To insert gaps using indices based on numbering after the insertion, see addGapsByIndices.
padAlignment()

Insert gaps into an alignment so that it forms a rectangular block

getGapOnlyColumns()

Returns a list of lists of indices columns that contain only gaps

Return type:list
Returns:List of list of indices
minimizeAlignment()

Minimizes the alignment, i.e. removes all gaps from the gap-only columns.

getColumn(index, omit_gaps=False)

Returns single alignment column at index position. Optionally, filters out gaps if omit_gaps is True.

Parameters:
  • index (int) – The index in the alignment
  • omit_gaps (bool) – Whether to omit the gaps
Returns:

Single alignment column at index position. Returns None to represent terminal gaps.
Return type:

tuple(residue.Residue or residue.Gap or None)
columns(omit_gaps=False)

A generator over all columns.

Parameters:omit_gaps (bool) – Whether to omit gaps
columnHasAllSameResidues(index)

Return whether or not the column at a specified index has all the same residues (excluding gaps).

Note that if any unknown residues are present, the column will not be considered to be of all the same residue type.

Parameters:index (int) – Index to check for uniformity`
Returns:True if the column is of uniform identity, False otherwise.
Return type:bool
getIdentities(omit_gaps=True)

Returns an alignment-length list of bools indicating which columns have identical residues

Parameters:omit_gaps (bool) – Whether gaps should be excluded from a column.
getSimilarityScore(seq)

Returns a sequence length array of similarity scores against the reference sequence

Gaps in the sequences are coded as None values.

getAlignedBlocks()

Returns the indices of aligned blocks (regions without gaps).

getFrequencies(exclude=None, consider_gaps=False)

Returns a dict mapping residues types to the frequency in the alignment

Parameters:
  • exclude (list) – A list of sequences to exclude
  • consider_gaps (bool) – Whether to consider gaps in calculating frequences
getEntropy(frequencies)

Returns an alignment length array of residue entropy scores

getRedundantSequences(value)

Returns the indices of sequences below a specified identity threshold value.

Returns:The indices of sequences in the alignment below specified identity threshold
Return type:list of int
calculateMatrix()

Calculates a substitution matrix based on the current alignment.

class schrodinger.protein.alignment.ProteinAlignment(*args, **kwargs)

Bases: schrodinger.models.json.JsonableClassMixin, schrodinger.protein.alignment.BaseAlignment

global_annotations

Returns the alignment-level annotations available for the alignment

seq_annotations

Returns the sequence-level annotations available for sequences held in the alignment

disulfide_bonds
toJsonImplementation()

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns:A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders
classmethod fromJsonImplementation(json_obj)

Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.

Parameters:json_dict (dict) – A dictionary loaded from a JSON string or file.
Returns:An instance of the derived class.

:rtype : cls

setHydrophobicityWindowPadding(window_padding)

Sets hydrophobicity window padding value for each sequence in the protein alignment.

Parameters:window_padding (int) – number of values to pad each average with
setIsoelectricPointWindowPadding(window_padding)

Sets isoelectric point window padding value for each sequence in the protein alignment.

Parameters:window_padding (int) – number of values to pad each average with
addDisulfideBond(res1, res2)

Add a disulfide bond if both residues’ sequences are in the alignment

Parameters:
Raises:

ValueError – if either sequence is not in the alignment
removeDisulfideBond(res1, res2)

Remove a disulfide bond if both residues’ sequences are in the alignment

Parameters:
Raises:

ValueError – if either sequence is not in the alignment
static fromClustalFile(file_name)

Returns alignment read from file in Clustal .aln format preserving order of sequences.

Parameters:file_name (str) – Source file name.
Raises:IOError – If output file cannot be read.
Return type:ProteinAlignment
Returns:An alignment
Note:The alignment can be empty if no sequence was present in the input file.
toClustalFile(file_name, use_unique_names=True)

Writes aln to a Clustal alignment file.

Raises:

IOError – If output file cannot be written.
Parameters:
  • file_name (str) – Destination file name.
  • use_unique_names (bool) – If True, write unique name for each sequence.
classmethod fromFastaFile(file_name)

Returns alignment read from file in Clustal .aln format preserving order of sequences.

Raises:IOError – If the input file cannot be read.
Parameters:file_name (str) – name of input FASTA file
Returns:Read alignment. The alignment can be empty if no sequence was present in the input file.
Return type:ProteinAlignment
classmethod fromFastaString(lines)

Read sequences from FASTA-formatted text, creates sequences and appends them to alignment. Splits sequence name from the FASTA header.

Parameters:lines (list of str) – list of strings representing FASTA file
Returns:The alignment
Return type:ProteinAlignment
classmethod fromFastaStringList(strings)

Return an alignment object created from an iterable of sequence strings

Parameters:strings (Iterable of strings) – Sequences as iterable of strings (1D codes)
Returns:The alignment
Return type:ProteinAlignment
toFastaString(use_unique_names=True, maxl=50)

Convert ProteinAlignment object to list of sequence strings

Parameters:aln (ProteinAlignment) – Alignment data
toFastaStringList()

Convert self to list of fasta sequence strings

Return type:list
Returns:list of str
toFastaFile(file_name, use_unique_names=True, maxl=50)

Write self to specified FASTA file

Raises:IOError – If output file cannot be written.
findPattern(pattern)

Finds a specified PROSITE pattern in all sequences.

Parameters:pattern (str) – PROSITE pattern to search in sequences. See protein.sequence.find_generalized_pattern for documentation.
Returns:List of matching residues
Return type:list of protein.residue.Residue
clearAllCaching()
class schrodinger.protein.alignment.NucleicAcidAlignment(sequences=None)

Bases: schrodinger.protein.alignment.BaseAlignment